Nav interface change = HELL YES, especially if you ARE looking to get the M3 with I-drive system.
So much better with hard drive CIC navi (09+), music storage, updated navigation, just so much easier button layout which stays the same way until now in all BMW lineups

If one's budget is 35~39K, push yourself and get a ~40K 08 model.
If the budget is 38~42K, push yourself and get a 42~46K 09 model.